Author: ruschein
Date: 2011-02-01 08:36:29 -0800 (Tue, 01 Feb 2011)
New Revision: 23987
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
core3/sbml-impl/trunk/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
core3/table-browser-impl/trunk/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/NetworkLineParser.java
core3/vizmap-gui-impl/trunk/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
Log:
Renamed getDataTable() in CyRow to getTable().
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -166,12 +166,12 @@
private void cloneRow(final CyRow from, final CyRow to) {
try {
- eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, to.getDataTable()));
+ eventHelper.fireSynchronousEvent(new
RowsAboutToChangeEvent(this, to.getTable()));
- for (final CyColumn column :
from.getDataTable().getColumns())
+ for (final CyColumn column :
from.getTable().getColumns())
to.set(column.getName(),
from.getRaw(column.getName()));
} finally {
- eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, to.getDataTable()));
+ eventHelper.fireSynchronousEvent(new
RowsFinishedChangingEvent(this, to.getTable()));
}
}
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/VisualStyleBuilder.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -183,7 +183,7 @@
String colName = getAttrName(vp);
// add a column to the table if it does not exist yet
- final CyTable table = row.getDataTable();
+ final CyTable table = row.getTable();
if (table.getColumn(colName) == null)
table.createColumn(colName, String.class, false);
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/AttributeValueUtil.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -302,8 +302,8 @@
// must make sure to clear out any existing values before we
parse.
case LIST:
manager.currentAttributeID = name;
- if (cyAtts.getDataTable().getColumn(name) != null
- && cyAtts.getDataTable().getColumn(name).getType()
== List.class)
+ if (cyAtts.getTable().getColumn(name) != null
+ && cyAtts.getTable().getColumn(name).getType() ==
List.class)
cyAtts.set(name, null);
return ParseState.LISTATT;
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -329,7 +329,7 @@
// Now handle all of the other network attributes
CyRow row = network.getCyRow();
- CyTable table = row.getDataTable();
+ CyTable table = row.getTable();
for (final CyColumn column : table.getColumns())
writeAttribute(row, column.getName());
@@ -365,7 +365,7 @@
// Output the node attributes
// TODO This isn't handling namespaces
- for (final CyColumn column :
node.getCyRow().getDataTable().getColumns())
+ for (final CyColumn column :
node.getCyRow().getTable().getColumns())
writeAttribute(node.getCyRow(), column.getName());
// TODO deal with groups
@@ -568,7 +568,7 @@
// Write the edge attributes
// TODO This isn't handling namespaces
- for (final CyColumn column :
curEdge.getCyRow().getDataTable().getColumns())
+ for (final CyColumn column :
curEdge.getCyRow().getTable().getColumns())
writeAttribute(curEdge.getCyRow(), column.getName());
// Write the edge graphics
@@ -657,7 +657,7 @@
*/
private void writeAttribute(final CyRow row, final String attName) throws
IOException {
// create an attribute and its type:
- final CyColumn column = row.getDataTable().getColumn(attName);
+ final CyColumn column = row.getTable().getColumn(attName);
if (column == null)
return;
final Class<?> attType = column.getType();
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/EdgeWeighter.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -112,7 +112,7 @@
// System.out.println("Setting weight for "+layoutEdge+" using
"+weightAttribute);
if (weightAttribute != null && row.isSet(weightAttribute)) {
- final Class<?> type =
row.getDataTable().getColumn(weightAttribute).getType();
+ final Class<?> type =
row.getTable().getColumn(weightAttribute).getType();
if (type == Integer.class) {
Integer val = row.get(weightAttribute,
Integer.class);
eValue = (double) val.intValue();
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/LayoutTask.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -63,7 +63,7 @@
// update the __layoutAlgorithm attribute
final CyRow networkAttributes =
network.getCyRow(CyNetwork.HIDDEN_ATTRS);
- final CyTable netAttrsTable = networkAttributes.getDataTable();
+ final CyTable netAttrsTable = networkAttributes.getTable();
if (netAttrsTable.getColumn(LAYOUT_ALGORITHM) == null)
netAttrsTable.createColumn(LAYOUT_ALGORITHM,
String.class, true);
networkAttributes.set(LAYOUT_ALGORITHM, name);
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayoutTask.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -57,7 +57,7 @@
if (this.attribute != null && count > 0) {
final CyColumn column =
-
nodes.get(0).getNode().getCyRow().getDataTable().getColumn(attribute);
+
nodes.get(0).getNode().getCyRow().getTable().getColumn(attribute);
Class<?> klass = (column == null) ? null :
column.getType();
if (klass != null &&
Comparable.class.isAssignableFrom(klass)){
// FIXME: I assume this would be better, but
get type errors if I try:
Modified: core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
===================================================================
--- core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
2011-02-01 01:40:10 UTC (rev 23986)
+++ core3/model-api/trunk/src/main/java/org/cytoscape/model/CyRow.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -95,5 +95,5 @@
* Returns the {@link CyTable} that this row belongs to.
* @return the {@link CyTable} that this row belongs to.
*/
- CyTable getDataTable();
+ CyTable getTable();
}
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -107,10 +107,10 @@
CyNode n2 = net.addNode();
CyEdge e1 = net.addEdge(n1,n2,true);
- assertEquals(String.class,
e1.getCyRow().getDataTable().getColumn("name").getType());
+ assertEquals(String.class,
e1.getCyRow().getTable().getColumn("name").getType());
assertEquals(Boolean.class,
-
e1.getCyRow().getDataTable().getColumn("selected").getType());
+
e1.getCyRow().getTable().getColumn("selected").getType());
assertEquals(String.class,
-
e1.getCyRow().getDataTable().getColumn("interaction").getType());
+
e1.getCyRow().getTable().getColumn("interaction").getType());
}
}
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -934,7 +934,7 @@
* Make sure the proper default attributes are created
*/
public void testDefaultAttributes() {
- assertEquals(String.class,
net.getCyRow().getDataTable().getColumn("name").getType());
+ assertEquals(String.class,
net.getCyRow().getTable().getColumn("name").getType());
}
public void testGetDefaultNetworkTable() {
Modified:
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
===================================================================
---
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/model-api/trunk/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -63,9 +63,9 @@
public void testDefaultAttributes() {
CyNode n1 = net.addNode();
assertEquals(String.class,
-
n1.getCyRow().getDataTable().getColumn("name").getType());
+
n1.getCyRow().getTable().getColumn("name").getType());
assertEquals(Boolean.class,
-
n1.getCyRow().getDataTable().getColumn("selected").getType());
+
n1.getCyRow().getTable().getColumn("selected").getType());
}
// by default a node should have a null nested network
Modified:
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
===================================================================
---
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/model-impl/trunk/impl/src/main/java/org/cytoscape/model/internal/CyTableImpl.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -892,7 +892,7 @@
}
@Override
- public CyTable getDataTable() {
+ public CyTable getTable() {
return table;
}
Modified:
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
===================================================================
---
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/network-analyzer-impl/trunk/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/ui/MapParameterDialog.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -486,7 +486,7 @@
for (int i = 0; i < attr.length; i++) {
for (int j = 0; j < attr[i].length; j++) {
final Class<?> attrType =
-
entry.getCyRow().getDataTable().getColumn(attr[i][j]).getType();
+
entry.getCyRow().getTable().getColumn(attr[i][j]).getType();
Double attrValue = new Double(0.0);
if (attrType == Integer.class)
Modified:
core3/sbml-impl/trunk/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
===================================================================
---
core3/sbml-impl/trunk/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/sbml-impl/trunk/src/main/java/org/cytoscape/sbml/internal/SBMLNetworkViewReader.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -177,8 +177,8 @@
}
private <T> void checkSchema(CyRow attributes, String attributeName,
Class<T> type) {
- if (attributes.getDataTable().getColumn(attributeName) == null)
- attributes.getDataTable().createColumn(attributeName,
type, false);
+ if (attributes.getTable().getColumn(attributeName) == null)
+ attributes.getTable().createColumn(attributeName, type,
false);
}
private static String readString(InputStream source) throws IOException
{
Modified:
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
===================================================================
---
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/search-impl/trunk/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -104,7 +104,7 @@
doc.add(new Field(EnhancedSearch.TYPE_FIELD, graphObjectType,
Field.Store.YES, Field.Index.ANALYZED));
CyRow cyRow = graphObject.getCyRow();
- CyTable cyDataTable = cyRow.getDataTable();
+ CyTable cyDataTable = cyRow.getTable();
Set<String> attributeNames =
CyTableUtil.getColumnNames(cyDataTable);
for (final String attrName : attributeNames) {
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkPanel.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -349,7 +349,7 @@
removeNetwork(net.getSUID());
RowSetMicroListener rsml = nameListeners.remove(net);
if ( rsml != null )
- eventHelper.removeMicroListener( rsml,
RowSetMicroListener.class, net.getCyRow().getDataTable() );
+ eventHelper.removeMicroListener( rsml,
RowSetMicroListener.class, net.getCyRow().getTable() );
}
public void handleEvent(NetworkAddedEvent e) {
Modified:
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
===================================================================
---
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/swing-application-impl/trunk/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -387,7 +387,7 @@
presentationContainerMap.remove(view.getModel().getSUID());
RowSetMicroListener rsml =
nameListeners.remove(view.getModel());
if ( rsml != null )
- eventHelper.removeMicroListener(rsml,
RowSetMicroListener.class, view.getModel().getCyRow().getDataTable());
+ eventHelper.removeMicroListener(rsml,
RowSetMicroListener.class, view.getModel().getCyRow().getTable());
}
/**
Modified:
core3/table-browser-impl/trunk/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
===================================================================
---
core3/table-browser-impl/trunk/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/table-browser-impl/trunk/src/main/java/org/cytoscape/browser/internal/BrowserTableModel.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -244,7 +244,7 @@
}
private static Object getColumnValue(final CyRow row, final String
columnName) {
- final CyColumn column =
row.getDataTable().getColumn(columnName);
+ final CyColumn column = row.getTable().getColumn(columnName);
if (column.getType() == List.class) {
final Class<?> listElementType =
column.getListElementType();
return row.getList(columnName, listElementType);
Modified:
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/NetworkLineParser.java
===================================================================
---
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/NetworkLineParser.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/table-import-impl/trunk/src/main/java/org/cytoscape/tableimport/internal/reader/NetworkLineParser.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -152,8 +152,8 @@
private void createColumn(final CyEdge edge, final String
attributeName, Class<?> theType){
// If attribute does not exist, create it
- if (edge.getCyRow().getDataTable().getColumn(attributeName) ==
null)
-
edge.getCyRow().getDataTable().createColumn(attributeName, theType, false);
+ if (edge.getCyRow().getTable().getColumn(attributeName) == null)
+ edge.getCyRow().getTable().createColumn(attributeName,
theType, false);
}
/**
Modified:
core3/vizmap-gui-impl/trunk/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
===================================================================
---
core3/vizmap-gui-impl/trunk/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
2011-02-01 01:40:10 UTC (rev 23986)
+++
core3/vizmap-gui-impl/trunk/src/main/java/org/cytoscape/view/vizmap/gui/internal/VizMapPropertyBuilder.java
2011-02-01 16:36:29 UTC (rev 23987)
@@ -193,7 +193,7 @@
final SortedSet<K> attrSet = new TreeSet<K>();
for (CyTableEntry go : graphObjectSet) {
final Class<?> attrClass =
-
go.getCyRow().getDataTable().getColumn(attrName).getType();
+
go.getCyRow().getTable().getColumn(attrName).getType();
Object id = go.getCyRow().get(attrName,
attrClass);
if (id != null)
@@ -238,7 +238,7 @@
for (CyTableEntry go : graphObjectSet) {
Class<?> attrClass =
-
go.getCyRow().getDataTable().getColumn(attrName).getType();
+
go.getCyRow().getTable().getColumn(attrName).getType();
id = go.getCyRow().get("name", String.class);
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